From 82f950ca97f8976fefcb7304fe86959cc52a8651 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Fri, 10 Jan 2025 19:22:46 +0100 Subject: [PATCH 1/3] add description of loading runs from nf-tower for debugging --- CONTRIBUTING.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index abf8c374..df3f55ec 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -146,3 +146,18 @@ To run the benchmark, you can use the following command: ```bash scripts/run_benchmark/run.sh ``` + +## Debugging nf-tower runs + +The actual benchmark is run on the [nf-tower platform](https://cloud.seqera.io/orgs/openproblems-bio/workspaces/openproblems-bio/watch). +You can find runs related to the batch integration by filtering for `label:task_batch_integration`, selecting a specific run and browsing the outputs. + +For debugging purposes, you can download the output of a task run from nf-tower following command: + +```bash +common/scripts/fetch_task_run \ + --input s3://openproblems-work/work/\ + --output temp_output +``` + +You can find the process ID under the "Work directory" section of the Task details. \ No newline at end of file From 0ee7b34377dcff6243d2bbeebcbba898a79165a4 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Fri, 10 Jan 2025 19:34:31 +0100 Subject: [PATCH 2/3] use working branch for extended cell cycle genes --- src/metrics/cell_cycle_conservation/config.vsh.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/metrics/cell_cycle_conservation/config.vsh.yaml b/src/metrics/cell_cycle_conservation/config.vsh.yaml index 493b814e..27b6111a 100644 --- a/src/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/metrics/cell_cycle_conservation/config.vsh.yaml @@ -28,7 +28,7 @@ info: doi: 10.1038/s41592-021-01336-8 links: homepage: https://scib.readthedocs.io/en/latest/ - documentation: https://scib.readthedocs.io/en/latest/api/scib.metrics.silhouette_batch.html + documentation: https://scib.readthedocs.io/en/latest/api/scib.metrics.cell_cycle.html repository: https://github.com/theislab/scib min: 0 max: 1 @@ -43,7 +43,7 @@ engines: setup: - type: python pypi: - - scib==1.1.5 + - git+https://github.com/theislab/scib.git@extend_cell_cycle_genes runners: - type: executable - type: nextflow From 289447583ef65c4164d1def554e29cd679904fa2 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Fri, 10 Jan 2025 19:47:30 +0100 Subject: [PATCH 3/3] update scib version for kbet --- src/metrics/kbet/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/metrics/kbet/config.vsh.yaml b/src/metrics/kbet/config.vsh.yaml index 71a7e8f6..428571cf 100644 --- a/src/metrics/kbet/config.vsh.yaml +++ b/src/metrics/kbet/config.vsh.yaml @@ -50,7 +50,7 @@ engines: github: theislab/kBET - type: python pypi: - - scib==1.1.5 + - scib==1.1.6 - rpy2>=3 - anndata2ri - scipy<=1.13